Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003903.1 Kokia drynarioides strain JFW-HI SEQ_116963, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2451
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27


Found at i:379 original size:206 final size:205

Alignment explanation


    Indices: 5--380  Score: 511
    Period size: 206  Copynumber: 1.8  Consensus size: 205

          1 TGAT

                *   *                            *     *             *       
          5 GAGATACTGAGAAGAAGACCAAATCAAACCCACGCCCTATGTGTGCAAATCTTCGAATCCCAGCT
          1 GAGACACTAAGAAGAAGACCAAATCAAACCCACGCCCGATGTGAGCAAATCTTCGAACCCCAGCT

                       *            *        *                      *    *   
         70 TCCTAATGAGATACTGAGAAGCAGGGTGAAGCAGTAAAAGGTTAGCTTCCTAATGAGATACTGAG
         66 TCCTAATGAGACACTGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTTCCTAATGAAATACGGAG

                 *      ** *   *   *    *                                    
        135 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAGAAACGATGCTGTCA
        131 AAGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAGCGAATTGAAAGAAACGATGCTGTCA

                      
        200 TCTTCCTGAC
        196 TCTTCCTGAC

                                                *                            
        210 GAGACACTAAGAAGAAGACCAAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGC
          1 GAGACACTAAGAAGAAGACC-AAATCAAACCCACGCCCGATGTGAGCAAATCTTCGAACCCCAGC

               * *                                *              *           
        275 TTCTTGATGAGACACTGAGAAGCA-AGTCGAAGCAATACAAGGTTAGCTTCCTGATGAAATACGG
         65 TTCCTAATGAGACACTGAGAAGCAGAGT-GAAGCAATAAAAGGTTAGCTTCCTAATGAAATACGG

            *  *                                      
        339 GGAGGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAG
        129 AGAAGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAG

        381 TGGATCAAAA


Statistics
Matches: 145,  Mismatches: 24, Indels: 3
        0.84            0.14        0.02

Matches are distributed among these distances:
 205   20  0.14
 206  125  0.86

ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20


Consensus pattern (205 bp):   
GAGACACTAAGAAGAAGACCAAATCAAACCCACGCCCGATGTGAGCAAATCTTCGAACCCCAGCT
TCCTAATGAGACACTGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTTCCTAATGAAATACGGAG
AAGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAGCGAATTGAAAGAAACGATGCTGTCA
TCTTCCTGAC

Found at i:431 original size:206 final size:205

Alignment explanation


    Indices: 5--437  Score: 471
    Period size: 206  Copynumber: 2.1  Consensus size: 205

          1 TGAT

                                                  *     *             *      
          5 GAGATACTGAGAAGAAGACC-AAATCAAACCCACGCCCTATGTGTGCAAATCTTCGAATCCCAGC
          1 GAGATACTGAGAAGAAGACCAAAATCAAACCCACGCCCGATGTGAGCAAATCTTCGAACCCCAGC

                        *            *        *                      *    *  
         69 TTCCTAATGAGATACTGAGAAGCAGGGTGAAGCAGTAAAAGGTTAGCTTCCTAATGAGATACTGA
         66 TTCCTAATGAGACACTGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTTCCTAATGAAATACGGA

                  *      ** *   *   *    *                **   *    *        
        134 GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAGAAACGATGCTGTC
        131 GAAGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAGCGAATCAAAACAAACAATGC-GTC

                    *  
        199 ATCTTCCTGAC
        195 ATCTTCCTAAC

                *   *                           *                            
        210 GAGACACTAAGAAGAAGACCAAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGC
          1 GAGATACTGAGAAGAAGACCAAAATCAAACCCACGCCCGATGTGAGCAAATCTTCGAACCCCAGC

               * *                                *              *           
        275 TTCTTGATGAGACACTGAGAAGCA-AGTCGAAGCAATACAAGGTTAGCTTCCTGATGAAATACGG
         66 TTCCTAATGAGACACTGAGAAGCAGAGT-GAAGCAATAAAAGGTTAGCTTCCTAATGAAATACGG

            *  *                                      * *                    
        339 GGAGGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAGTGGATCAAAACAAGTTA-AATG-
        130 AGAAGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAGCGAATCAAAACAA---ACAATGC

               *    *      
        402 GTCGTCTTGCTAATC
        192 GTCATCTTCCTAA-C

                             *    
        417 -AGATACTGAGAAGAAGGCCAA
          1 GAGATACTGAGAAGAAGACCAA

        438 GTCAATGAAA


Statistics
Matches: 186,  Mismatches: 36, Indels: 11
        0.80            0.15        0.05

Matches are distributed among these distances:
 205   20  0.11
 206  161  0.87
 207    1  0.01
 208    3  0.02
 209    1  0.01

ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20


Consensus pattern (205 bp):   
GAGATACTGAGAAGAAGACCAAAATCAAACCCACGCCCGATGTGAGCAAATCTTCGAACCCCAGC
TTCCTAATGAGACACTGAGAAGCAGAGTGAAGCAATAAAAGGTTAGCTTCCTAATGAAATACGGA
GAAGTGAACCAAAACCATCTCCCTAATGAAATACAGAGAAGCGAATCAAAACAAACAATGCGTCA
TCTTCCTAAC

Found at i:960 original size:18 final size:18

Alignment explanation


    Indices: 937--978  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

        927 CCCAAATAAA

                              
        937 CAAATTACACCCCAAACC
          1 CAAATTACACCCCAAACC

                     * * *    
        955 CAAATTACATCTCTAACC
          1 CAAATTACACCCCAAACC

                  
        973 CAAATT
          1 CAAATT

        979 CACAAGTCAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21


Consensus pattern (18 bp):   
CAAATTACACCCCAAACC
Done.